Starting phenix.real_space_refine on Thu May 15 06:48:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihm_35449/05_2025/8ihm_35449.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 317 5.49 5 S 12 5.16 5 C 7266 2.51 5 N 2473 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13153 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 607 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 801 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 711 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 779 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ML3:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 609 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 760 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 639 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3216 Classifications: {'DNA': 158} Link IDs: {'rna3p': 157} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3280 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 154 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "N" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 841 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 8.38, per 1000 atoms: 0.64 Number of scatterers: 13153 At special positions: 0 Unit cell: (93.09, 140.17, 116.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 317 15.00 O 3085 8.00 N 2473 7.00 C 7266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.0 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 20 Warning! O4 atom is missing from residue DT I 31 Was trying to link: DA J -31 N6 with DT I 31 O4, Saenger class: 23 Secondary structure from input PDB file: 39 helices and 9 sheets defined 65.6% alpha, 4.2% beta 150 base pairs and 238 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.569A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 115 removed outlier: 3.861A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 130 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.650A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 4.228A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.776A pdb=" N TYR B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.771A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.651A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.560A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.561A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.553A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 74 removed outlier: 3.963A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 81 Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.830A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.769A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.710A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.581A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.673A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.656A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.621A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.692A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.738A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 54 through 81 removed outlier: 3.778A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP H 65 " --> pdb=" O SER H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.533A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU H 97 " --> pdb=" O THR H 93 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.568A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 74 removed outlier: 4.358A pdb=" N GLY N 74 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 131 removed outlier: 3.570A pdb=" N LYS N 108 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS N 120 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN N 125 " --> pdb=" O SER N 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.052A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.051A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.177A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.440A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.589A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'N' and resid 79 through 81 removed outlier: 3.588A pdb=" N LEU N 21 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA N 16 " --> pdb=" O TYR N 23 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 14 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU N 15 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 29 through 32 removed outlier: 4.445A pdb=" N ASP N 32 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET N 37 " --> pdb=" O ASP N 32 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 238 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2231 1.33 - 1.45: 4788 1.45 - 1.57: 6363 1.57 - 1.69: 632 1.69 - 1.81: 22 Bond restraints: 14036 Sorted by residual: bond pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" SG ML3 E 36 " pdb=" CD ML3 E 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" CA ALA D 74 " pdb=" C ALA D 74 " ideal model delta sigma weight residual 1.524 1.458 0.066 2.25e-02 1.98e+03 8.52e+00 bond pdb=" CA TYR A 99 " pdb=" C TYR A 99 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.35e-02 5.49e+03 7.10e+00 bond pdb=" CB ML3 E 36 " pdb=" SG ML3 E 36 " ideal model delta sigma weight residual 1.817 1.765 0.052 2.00e-02 2.50e+03 6.66e+00 ... (remaining 14031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 19972 2.30 - 4.60: 323 4.60 - 6.89: 29 6.89 - 9.19: 6 9.19 - 11.49: 2 Bond angle restraints: 20332 Sorted by residual: angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 111.81 102.06 9.75 8.60e-01 1.35e+00 1.29e+02 angle pdb=" N ARG N 98 " pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 109.72 98.23 11.49 1.60e+00 3.91e-01 5.15e+01 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" C GLU A 97 " ideal model delta sigma weight residual 111.40 103.25 8.15 1.22e+00 6.72e-01 4.46e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.14 104.49 6.65 1.08e+00 8.57e-01 3.80e+01 angle pdb=" N ILE N 72 " pdb=" CA ILE N 72 " pdb=" C ILE N 72 " ideal model delta sigma weight residual 112.50 119.83 -7.33 1.39e+00 5.18e-01 2.78e+01 ... (remaining 20327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.51: 6045 35.51 - 71.01: 1493 71.01 - 106.52: 42 106.52 - 142.02: 4 142.02 - 177.53: 3 Dihedral angle restraints: 7587 sinusoidal: 5027 harmonic: 2560 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C4' DC I -73 " pdb=" C3' DC I -73 " pdb=" O3' DC I -73 " pdb=" P DT I -72 " ideal model delta sinusoidal sigma weight residual -140.00 37.53 -177.53 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 56.50 163.50 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1368 0.032 - 0.064: 678 0.064 - 0.096: 185 0.096 - 0.128: 61 0.128 - 0.160: 9 Chirality restraints: 2301 Sorted by residual: chirality pdb=" CA ARG N 98 " pdb=" N ARG N 98 " pdb=" C ARG N 98 " pdb=" CB ARG N 98 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ALA D 74 " pdb=" N ALA D 74 " pdb=" C ALA D 74 " pdb=" CB ALA D 74 " both_signs ideal model delta sigma weight residual False 2.48 2.34 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 2298 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 63 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLU F 63 " 0.039 2.00e-02 2.50e+03 pdb=" O GLU F 63 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN F 64 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO A 66 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 8 " -0.027 2.00e-02 2.50e+03 1.23e-02 4.57e+00 pdb=" N9 DG J 8 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DG J 8 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DG J 8 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DG J 8 " -0.010 2.00e-02 2.50e+03 pdb=" O6 DG J 8 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 8 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 8 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG J 8 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG J 8 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 8 " 0.001 2.00e-02 2.50e+03 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3530 2.82 - 3.34: 13386 3.34 - 3.86: 25816 3.86 - 4.38: 29084 4.38 - 4.90: 39690 Nonbonded interactions: 111506 Sorted by model distance: nonbonded pdb=" O ILE M 54 " pdb=" OG1 THR M 55 " model vdw 2.297 3.040 nonbonded pdb=" C3' DT I 71 " pdb=" C1' DT I 71 " model vdw 2.319 3.120 nonbonded pdb=" OP1 DT I 12 " pdb=" N GLY N 83 " model vdw 2.365 3.120 nonbonded pdb=" N3 DC I -73 " pdb=" N2 DG J 74 " model vdw 2.372 3.200 nonbonded pdb=" O SER M 62 " pdb=" OG SER M 62 " model vdw 2.399 3.040 ... (remaining 111501 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 38 through 45 or (resid 46 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 through 62 or (r \ esid 63 and (name N or name CA or name C or name O or name CB )) or resid 64 thr \ ough 70 or (resid 71 through 72 and (name N or name CA or name C or name O or na \ me CB )) or resid 73 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 89 or (resid 90 through 91 and (name N \ or name CA or name C or name O or name CB )) or resid 92 through 96 or (resid 9 \ 7 through 98 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 9 or (resid 100 through 102 and (name N or name CA or name C or name O or name C \ B )) or resid 103 or (resid 104 through 108 and (name N or name CA or name C or \ name O or name CB )) or resid 109 through 134)) selection = (chain 'E' and (resid 38 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB )) or resid 52 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 67 or (resid 68 and ( \ name N or name CA or name C or name O or name CB )) or resid 69 through 74 or (r \ esid 75 and (name N or name CA or name C or name O )) or resid 76 through 87 or \ (resid 88 and (name N or name CA or name C or name O )) or resid 89 through 104 \ or (resid 105 through 108 and (name N or name CA or name C or name O or name CB \ )) or resid 109 through 114 or (resid 115 through 116 and (name N or name CA or \ name C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA \ or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or nam \ e CA or name C or name O or name CB )) or resid 121 through 134)) } ncs_group { reference = (chain 'B' and (resid 22 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 29 or (resid 30 through 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 35 or (res \ id 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 50 or (resid 51 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 52 th \ rough 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) o \ r resid 63 through 64 or (resid 65 through 67 and (name N or name CA or name C o \ r name O or name CB )) or resid 68 through 77 or (resid 78 through 80 and (name \ N or name CA or name C or name O or name CB )) or resid 81 or (resid 82 through \ 83 and (name N or name CA or name C or name O or name CB )) or resid 84 or (resi \ d 85 and (name N or name CA or name C or name O or name CB )) or resid 86 throug \ h 101)) selection = (chain 'F' and (resid 22 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 34 or (resid 35 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name NE or name CZ \ or name NH1)) or resid 36 through 44 or (resid 45 through 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 70 or (resid 71 and (n \ ame N or name CA or name C or name O or name CB )) or resid 72 or (resid 73 and \ (name N or name CA or name C or name O or name CB )) or resid 74 through 90 or ( \ resid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 th \ rough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) o \ r resid 98 through 99 or (resid 100 and (name N or name CA or name C or name O o \ r name CB )) or resid 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 15 or (resid 16 and (name N or name CA or name \ C or name O )) or resid 17 through 24 or (resid 25 and (name N or name CA or nam \ e C or name O or name CB )) or resid 26 through 35 or (resid 36 and (name N or n \ ame CA or name C or name O or name CB )) or resid 37 through 40 or (resid 41 and \ (name N or name CA or name C or name O or name CB )) or resid 42 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1)) or resid 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 62 or (resid 63 and (name N \ or name CA or name C or name O or name CB )) or resid 64 through 76 or (resid 7 \ 7 through 78 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 9 through 80 or (resid 81 and (name N or name CA or name C or name O or name CB \ )) or resid 82 through 84 or (resid 85 through 87 and (name N or name CA or name \ C or name O or name CB )) or resid 88 through 89 or (resid 90 and (name N or na \ me CA or name C or name O or name CB )) or resid 91 through 94 or (resid 95 and \ (name N or name CA or name C or name O or name CB )) or resid 96 through 114 or \ (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 116 \ through 117)) selection = (chain 'G' and (resid 12 through 32 or (resid 33 through 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 48 or (resid 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 58 or (res \ id 59 through 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 77 or (resid 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB )) or resid 102 through 117)) } ncs_group { reference = (chain 'D' and ((resid 33 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 or (resid 57 through 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 84 or (re \ sid 85 and (name N or name CA or name C or name O or name CB )) or resid 86 or ( \ resid 87 through 90 and (name N or name CA or name C or name O or name CB )) or \ resid 91 through 121)) selection = (chain 'H' and (resid 33 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 59 or (resid 60 through 61 and (na \ me N or name CA or name C or name O or name CB )) or resid 62 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 83 or (resid 84 through 85 and (name N or name CA or name C or name O or name \ CB )) or resid 86 through 87 or (resid 88 through 90 and (name N or name CA or \ name C or name O or name CB )) or resid 91 through 111 or (resid 112 and (name N \ or name CA or name C or name O or name CB )) or resid 113 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.440 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 14036 Z= 0.343 Angle : 0.752 11.488 20332 Z= 0.469 Chirality : 0.041 0.160 2301 Planarity : 0.004 0.054 1495 Dihedral : 29.269 177.526 5929 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.23), residues: 861 helix: -2.84 (0.17), residues: 548 sheet: -2.63 (1.01), residues: 19 loop : -1.68 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 91 HIS 0.003 0.001 HIS N 18 PHE 0.023 0.002 PHE C 25 TYR 0.014 0.002 TYR D 37 ARG 0.006 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.20027 ( 751) hydrogen bonds : angle 8.02285 ( 1850) covalent geometry : bond 0.00726 (14036) covalent geometry : angle 0.75250 (20332) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.933 Fit side-chains REVERT: B 77 LYS cc_start: 0.8833 (mttm) cc_final: 0.8613 (mmtt) REVERT: C 38 ASN cc_start: 0.8345 (m110) cc_final: 0.7689 (m110) REVERT: E 94 GLU cc_start: 0.8384 (tp30) cc_final: 0.8150 (tp30) REVERT: F 84 MET cc_start: 0.8148 (tpp) cc_final: 0.7889 (tpp) REVERT: H 106 HIS cc_start: 0.8097 (m-70) cc_final: 0.7801 (m-70) REVERT: N 114 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8389 (tm-30) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3054 time to fit residues: 76.0050 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 79 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.120181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085564 restraints weight = 34092.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087623 restraints weight = 18035.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088906 restraints weight = 12701.280| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14036 Z= 0.222 Angle : 0.659 7.158 20332 Z= 0.384 Chirality : 0.038 0.136 2301 Planarity : 0.005 0.051 1495 Dihedral : 32.084 174.540 4413 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.77 % Allowed : 13.64 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.27), residues: 861 helix: -0.54 (0.21), residues: 581 sheet: -1.97 (1.01), residues: 19 loop : -1.26 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.012 0.002 PHE C 25 TYR 0.015 0.002 TYR F 88 ARG 0.004 0.000 ARG F 23 Details of bonding type rmsd hydrogen bonds : bond 0.05692 ( 751) hydrogen bonds : angle 4.01443 ( 1850) covalent geometry : bond 0.00493 (14036) covalent geometry : angle 0.65889 (20332) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.907 Fit side-chains REVERT: B 53 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 77 LYS cc_start: 0.9010 (mttm) cc_final: 0.8501 (mmtt) REVERT: B 98 TYR cc_start: 0.8749 (m-10) cc_final: 0.8540 (m-10) REVERT: D 73 GLU cc_start: 0.8104 (tp30) cc_final: 0.7894 (tp30) REVERT: D 120 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8627 (m) REVERT: E 81 ASP cc_start: 0.7927 (t0) cc_final: 0.7667 (t0) REVERT: H 106 HIS cc_start: 0.8034 (m-70) cc_final: 0.7586 (m-70) REVERT: N 37 MET cc_start: 0.7811 (ppp) cc_final: 0.7556 (ppp) REVERT: N 65 GLU cc_start: 0.4908 (tt0) cc_final: 0.4481 (tt0) REVERT: N 110 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7886 (mmp80) REVERT: N 114 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8162 (tm-30) outliers start: 11 outliers final: 7 residues processed: 161 average time/residue: 0.2590 time to fit residues: 58.8273 Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 0.0030 chunk 88 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN G 84 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.122871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088787 restraints weight = 33804.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.090670 restraints weight = 18200.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091910 restraints weight = 12866.779| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14036 Z= 0.161 Angle : 0.599 9.794 20332 Z= 0.350 Chirality : 0.035 0.172 2301 Planarity : 0.004 0.038 1495 Dihedral : 31.735 171.350 4413 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.57 % Allowed : 15.89 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.28), residues: 861 helix: 0.76 (0.22), residues: 575 sheet: -1.11 (1.14), residues: 19 loop : -0.89 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 31 HIS 0.006 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.001 TYR G 39 ARG 0.003 0.000 ARG F 55 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 751) hydrogen bonds : angle 3.18782 ( 1850) covalent geometry : bond 0.00347 (14036) covalent geometry : angle 0.59888 (20332) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.961 Fit side-chains REVERT: A 81 ASP cc_start: 0.8089 (m-30) cc_final: 0.7829 (p0) REVERT: B 22 LEU cc_start: 0.3566 (OUTLIER) cc_final: 0.3300 (pp) REVERT: B 53 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7990 (tm-30) REVERT: B 77 LYS cc_start: 0.8886 (mttm) cc_final: 0.8417 (mmtt) REVERT: B 98 TYR cc_start: 0.8745 (m-10) cc_final: 0.8449 (m-10) REVERT: D 73 GLU cc_start: 0.7950 (tp30) cc_final: 0.7688 (tp30) REVERT: E 81 ASP cc_start: 0.7729 (t0) cc_final: 0.7515 (t0) REVERT: G 35 ARG cc_start: 0.9129 (mtm-85) cc_final: 0.8224 (mtm-85) REVERT: G 97 LEU cc_start: 0.8067 (mp) cc_final: 0.7735 (mt) REVERT: H 106 HIS cc_start: 0.7356 (m90) cc_final: 0.7032 (m-70) REVERT: N 110 ARG cc_start: 0.8391 (mmp80) cc_final: 0.8068 (mmp80) REVERT: N 114 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8211 (tm-30) outliers start: 16 outliers final: 7 residues processed: 171 average time/residue: 0.2631 time to fit residues: 63.0362 Evaluate side-chains 155 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.120460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.085436 restraints weight = 33636.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087418 restraints weight = 18199.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.088636 restraints weight = 12983.907| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14036 Z= 0.210 Angle : 0.620 6.272 20332 Z= 0.360 Chirality : 0.037 0.146 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.801 174.628 4413 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.53 % Allowed : 17.34 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.29), residues: 861 helix: 1.06 (0.23), residues: 573 sheet: -1.26 (1.11), residues: 19 loop : -0.82 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 91 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.016 0.001 TYR F 88 ARG 0.003 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 751) hydrogen bonds : angle 3.26092 ( 1850) covalent geometry : bond 0.00471 (14036) covalent geometry : angle 0.62020 (20332) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8079 (m-30) cc_final: 0.7795 (p0) REVERT: B 22 LEU cc_start: 0.3423 (OUTLIER) cc_final: 0.3172 (pp) REVERT: B 53 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8109 (tm-30) REVERT: B 77 LYS cc_start: 0.8911 (mttm) cc_final: 0.8411 (mmtt) REVERT: E 81 ASP cc_start: 0.7823 (t0) cc_final: 0.7574 (t0) REVERT: G 35 ARG cc_start: 0.9160 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: H 81 ASN cc_start: 0.8102 (m-40) cc_final: 0.7870 (m-40) REVERT: H 106 HIS cc_start: 0.7606 (m90) cc_final: 0.7187 (m-70) REVERT: M 54 ILE cc_start: 0.4588 (OUTLIER) cc_final: 0.4325 (tt) REVERT: N 114 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8213 (tm-30) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.2967 time to fit residues: 61.5453 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 54 ILE Chi-restraints excluded: chain N residue 65 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 18 optimal weight: 0.2980 chunk 65 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.124129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089925 restraints weight = 33687.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091955 restraints weight = 17963.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.093207 restraints weight = 12704.053| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14036 Z= 0.147 Angle : 0.575 7.063 20332 Z= 0.338 Chirality : 0.034 0.146 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.424 177.291 4413 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.89 % Allowed : 19.10 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.29), residues: 861 helix: 1.46 (0.22), residues: 574 sheet: -1.18 (1.04), residues: 19 loop : -0.66 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 88 HIS 0.006 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.010 0.001 TYR N 100 ARG 0.004 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 751) hydrogen bonds : angle 2.81081 ( 1850) covalent geometry : bond 0.00319 (14036) covalent geometry : angle 0.57499 (20332) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2810 (pp) REVERT: B 77 LYS cc_start: 0.8802 (mttm) cc_final: 0.8325 (mmtt) REVERT: D 73 GLU cc_start: 0.7924 (tp30) cc_final: 0.7562 (tp30) REVERT: E 81 ASP cc_start: 0.7764 (t0) cc_final: 0.7544 (t0) REVERT: G 35 ARG cc_start: 0.9080 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: H 106 HIS cc_start: 0.7367 (m90) cc_final: 0.7027 (m-70) REVERT: H 112 THR cc_start: 0.9013 (m) cc_final: 0.8758 (p) REVERT: N 13 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6862 (mtm110) REVERT: N 24 GLU cc_start: 0.6462 (tp30) cc_final: 0.6068 (tp30) REVERT: N 90 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6934 (mm-30) REVERT: N 114 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7993 (tm-30) outliers start: 18 outliers final: 11 residues processed: 156 average time/residue: 0.2829 time to fit residues: 61.2132 Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.121315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086287 restraints weight = 34152.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088288 restraints weight = 18109.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089527 restraints weight = 12774.943| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14036 Z= 0.210 Angle : 0.619 7.431 20332 Z= 0.357 Chirality : 0.036 0.182 2301 Planarity : 0.004 0.044 1495 Dihedral : 31.576 173.805 4413 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.37 % Allowed : 18.94 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.29), residues: 861 helix: 1.51 (0.22), residues: 574 sheet: -1.19 (1.04), residues: 19 loop : -0.68 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 91 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.019 0.002 TYR F 88 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 751) hydrogen bonds : angle 3.06914 ( 1850) covalent geometry : bond 0.00471 (14036) covalent geometry : angle 0.61889 (20332) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.976 Fit side-chains REVERT: B 22 LEU cc_start: 0.3105 (OUTLIER) cc_final: 0.2785 (pp) REVERT: B 77 LYS cc_start: 0.8901 (mttm) cc_final: 0.8415 (mmtt) REVERT: B 98 TYR cc_start: 0.8820 (m-10) cc_final: 0.8478 (m-10) REVERT: D 73 GLU cc_start: 0.8056 (tp30) cc_final: 0.7850 (tp30) REVERT: E 81 ASP cc_start: 0.7839 (t0) cc_final: 0.7592 (t0) REVERT: E 94 GLU cc_start: 0.8257 (tp30) cc_final: 0.8027 (tp30) REVERT: F 88 TYR cc_start: 0.8455 (m-80) cc_final: 0.8161 (m-80) REVERT: G 35 ARG cc_start: 0.9105 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: H 106 HIS cc_start: 0.7534 (m90) cc_final: 0.7156 (m-70) REVERT: N 13 ARG cc_start: 0.7281 (mtm110) cc_final: 0.6846 (mtm110) REVERT: N 110 ARG cc_start: 0.8460 (mmp80) cc_final: 0.8005 (mmp80) REVERT: N 114 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8145 (tm-30) outliers start: 21 outliers final: 15 residues processed: 152 average time/residue: 0.3063 time to fit residues: 63.0831 Evaluate side-chains 153 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.123524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089038 restraints weight = 33540.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091013 restraints weight = 17953.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092220 restraints weight = 12713.424| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14036 Z= 0.163 Angle : 0.595 7.240 20332 Z= 0.346 Chirality : 0.035 0.166 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.430 173.127 4413 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.53 % Allowed : 18.78 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.29), residues: 861 helix: 1.67 (0.22), residues: 576 sheet: -0.59 (1.10), residues: 19 loop : -0.58 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.018 0.001 TYR F 88 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04437 ( 751) hydrogen bonds : angle 2.88229 ( 1850) covalent geometry : bond 0.00358 (14036) covalent geometry : angle 0.59547 (20332) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.020 Fit side-chains REVERT: B 22 LEU cc_start: 0.2884 (OUTLIER) cc_final: 0.2590 (pp) REVERT: B 77 LYS cc_start: 0.8854 (mttm) cc_final: 0.8365 (mmtt) REVERT: B 98 TYR cc_start: 0.8793 (m-10) cc_final: 0.8463 (m-10) REVERT: D 73 GLU cc_start: 0.8000 (tp30) cc_final: 0.7789 (tp30) REVERT: D 122 LYS cc_start: 0.6440 (tppt) cc_final: 0.6119 (tppt) REVERT: E 81 ASP cc_start: 0.7816 (t0) cc_final: 0.7575 (t0) REVERT: F 88 TYR cc_start: 0.8412 (m-80) cc_final: 0.8068 (m-80) REVERT: G 35 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8188 (mtm-85) REVERT: H 106 HIS cc_start: 0.7394 (m90) cc_final: 0.7067 (m-70) REVERT: N 13 ARG cc_start: 0.7356 (mtm110) cc_final: 0.6833 (mtm110) REVERT: N 90 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5768 (pt0) REVERT: N 110 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8044 (mmp80) REVERT: N 114 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8127 (tm-30) outliers start: 22 outliers final: 14 residues processed: 157 average time/residue: 0.3209 time to fit residues: 69.0432 Evaluate side-chains 151 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 26 optimal weight: 0.0010 chunk 53 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.124780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.090626 restraints weight = 33625.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.092616 restraints weight = 17795.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093864 restraints weight = 12523.246| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14036 Z= 0.151 Angle : 0.594 10.387 20332 Z= 0.342 Chirality : 0.034 0.160 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.324 171.604 4413 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.73 % Allowed : 19.58 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.29), residues: 861 helix: 1.86 (0.22), residues: 575 sheet: -0.60 (1.06), residues: 19 loop : -0.46 (0.37), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 88 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE E 67 TYR 0.018 0.001 TYR F 88 ARG 0.008 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 751) hydrogen bonds : angle 2.75661 ( 1850) covalent geometry : bond 0.00330 (14036) covalent geometry : angle 0.59406 (20332) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: B 22 LEU cc_start: 0.2777 (OUTLIER) cc_final: 0.2441 (pp) REVERT: B 77 LYS cc_start: 0.8822 (mttm) cc_final: 0.8355 (mmtt) REVERT: B 98 TYR cc_start: 0.8755 (m-10) cc_final: 0.8426 (m-10) REVERT: D 73 GLU cc_start: 0.7992 (tp30) cc_final: 0.7672 (tp30) REVERT: E 81 ASP cc_start: 0.7700 (t0) cc_final: 0.7484 (t0) REVERT: G 35 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8213 (mtm-85) REVERT: N 13 ARG cc_start: 0.7234 (mtm110) cc_final: 0.6925 (mtm110) REVERT: N 90 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5354 (pt0) REVERT: N 114 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8238 (tm-30) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.2826 time to fit residues: 59.4593 Evaluate side-chains 146 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 52 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.124462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090274 restraints weight = 33440.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092232 restraints weight = 17765.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093455 restraints weight = 12562.263| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14036 Z= 0.157 Angle : 0.608 9.720 20332 Z= 0.349 Chirality : 0.035 0.165 2301 Planarity : 0.004 0.042 1495 Dihedral : 31.319 171.559 4413 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.73 % Allowed : 20.06 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 861 helix: 1.90 (0.22), residues: 576 sheet: -0.32 (1.07), residues: 19 loop : -0.48 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 91 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR F 88 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04310 ( 751) hydrogen bonds : angle 2.77307 ( 1850) covalent geometry : bond 0.00347 (14036) covalent geometry : angle 0.60823 (20332) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.945 Fit side-chains REVERT: B 22 LEU cc_start: 0.2745 (OUTLIER) cc_final: 0.2422 (pp) REVERT: B 77 LYS cc_start: 0.8829 (mttm) cc_final: 0.8345 (mmtt) REVERT: B 98 TYR cc_start: 0.8736 (m-10) cc_final: 0.8388 (m-10) REVERT: D 73 GLU cc_start: 0.7955 (tp30) cc_final: 0.7621 (tp30) REVERT: D 122 LYS cc_start: 0.6351 (tppt) cc_final: 0.5979 (tppt) REVERT: E 81 ASP cc_start: 0.7708 (t0) cc_final: 0.7488 (t0) REVERT: G 35 ARG cc_start: 0.9015 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: M 52 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7817 (tmmt) REVERT: N 13 ARG cc_start: 0.7308 (mtm110) cc_final: 0.6836 (mtm110) REVERT: N 90 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5351 (pt0) REVERT: N 110 ARG cc_start: 0.8410 (mmp80) cc_final: 0.8050 (mmp80) REVERT: N 114 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8280 (tm-30) outliers start: 17 outliers final: 15 residues processed: 145 average time/residue: 0.2779 time to fit residues: 55.9686 Evaluate side-chains 150 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086204 restraints weight = 33575.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088074 restraints weight = 18305.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089229 restraints weight = 13141.988| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14036 Z= 0.243 Angle : 0.661 8.761 20332 Z= 0.375 Chirality : 0.038 0.171 2301 Planarity : 0.004 0.045 1495 Dihedral : 31.638 172.304 4413 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.41 % Allowed : 19.90 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 861 helix: 1.64 (0.22), residues: 574 sheet: -0.09 (1.16), residues: 19 loop : -0.73 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 91 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE M 63 TYR 0.014 0.002 TYR C 57 ARG 0.008 0.001 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 751) hydrogen bonds : angle 3.17821 ( 1850) covalent geometry : bond 0.00551 (14036) covalent geometry : angle 0.66103 (20332) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.938 Fit side-chains REVERT: B 22 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2570 (pp) REVERT: B 77 LYS cc_start: 0.8902 (mttm) cc_final: 0.8440 (mmtt) REVERT: B 98 TYR cc_start: 0.8826 (m-10) cc_final: 0.8498 (m-10) REVERT: D 73 GLU cc_start: 0.8055 (tp30) cc_final: 0.7700 (tp30) REVERT: D 122 LYS cc_start: 0.6559 (tppt) cc_final: 0.6340 (tppt) REVERT: E 81 ASP cc_start: 0.7988 (t0) cc_final: 0.7719 (t0) REVERT: G 35 ARG cc_start: 0.9111 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: H 53 SER cc_start: 0.8308 (p) cc_final: 0.7615 (m) REVERT: H 106 HIS cc_start: 0.7767 (m90) cc_final: 0.7262 (m-70) REVERT: M 52 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7760 (tmmt) REVERT: N 13 ARG cc_start: 0.7328 (mtm110) cc_final: 0.6954 (mtm110) REVERT: N 90 GLU cc_start: 0.5970 (mm-30) cc_final: 0.5416 (pt0) REVERT: N 110 ARG cc_start: 0.8414 (mmp80) cc_final: 0.8001 (mmp80) REVERT: N 114 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8171 (tm-30) outliers start: 15 outliers final: 14 residues processed: 147 average time/residue: 0.3178 time to fit residues: 63.1190 Evaluate side-chains 152 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 123 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.122946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088228 restraints weight = 33654.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090221 restraints weight = 18157.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.091451 restraints weight = 12919.878| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14036 Z= 0.158 Angle : 0.611 8.721 20332 Z= 0.351 Chirality : 0.035 0.178 2301 Planarity : 0.004 0.043 1495 Dihedral : 31.332 172.956 4413 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.25 % Allowed : 20.39 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 861 helix: 1.91 (0.22), residues: 576 sheet: 0.13 (1.19), residues: 19 loop : -0.56 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 91 HIS 0.005 0.001 HIS B 75 PHE 0.011 0.001 PHE E 67 TYR 0.012 0.001 TYR F 88 ARG 0.008 0.000 ARG G 71 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 751) hydrogen bonds : angle 2.81236 ( 1850) covalent geometry : bond 0.00348 (14036) covalent geometry : angle 0.61130 (20332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4140.53 seconds wall clock time: 72 minutes 50.74 seconds (4370.74 seconds total)